PDB-6azu: Holo IDO1 crystal structure

ID or keywords:

Entry

Database: PDB / ID: 6azu

Title

Holo IDO1 crystal structure

Components

Indoleamine 2,3-dioxygenase 1

Keywords

OXIDOREDUCTASE / holoenzyme IDO1

Function / homology

Function and homology information

indoleamine 2,3-dioxygenase / smooth muscle contractile fiber /

indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process /

tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.822 Å

Authors

Lewis, H.A. / Yan, C.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Immune-modulating enzyme indoleamine 2,3-dioxygenase is effectively inhibited by targeting its apo-form.
Authors: Nelp, M.T. / Kates, P.A. / Hunt, J.T. / Newitt, J.A. / Balog, A. / Maley, D. / Zhu, X. / Abell, L. / Allentoff, A. / Borzilleri, R. / Lewis, H.A. / Lin, Z. / Seitz, S.P. / Yan, C. / Groves, J.T.

History

Deposition	Sep 13, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 11, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6azu.cif.gz	557.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6azu.ent.gz	456.6 KB	Display	PDB format
PDBx/mmJSON format	6azu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/6azu ftp://data.pdbj.org/pub/pdb/validation_reports/az/6azu	HTTPS FTP

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Related structure data

Related structure data	6azvC 6azwC 2d0tS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4u74-2 6e45-4 6e43-2 6azv-1 5wn8-2 6azw-2 5wmx-2 6e46-2 6dpq-1 4u72-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6azvC

6azwC

2d0tS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Indoleamine 2,3-dioxygenase 1

B: Indoleamine 2,3-dioxygenase 1

C: Indoleamine 2,3-dioxygenase 1

D: Indoleamine 2,3-dioxygenase 1

hetero molecules

184 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Indoleamine 2,3-dioxygenase 1

hetero molecules

defined by author&software
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Indoleamine 2,3-dioxygenase 1

hetero molecules

defined by author&software
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Indoleamine 2,3-dioxygenase 1

hetero molecules

defined by author&software
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Indoleamine 2,3-dioxygenase 1

hetero molecules

defined by author&software
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.109, 177.513, 101.253
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Indoleamine 2,3-dioxygenase 1 / / IDO-1 / Indoleamine-pyrrole 2 / 3-dioxygenase Mass: 45254.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli (E. coli) / References: UniProt: P14902, indoleamine 2,3-dioxygenase
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / Details: 20% PEG-3350, 0.2 M LiSO4, 0.1 M BT pH 5.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-ID / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.822→34.023 Å / Num. all: 52390 / Num. obs: 52390 / % possible obs: 99.9 % / Redundancy: 6.6 % / B_iso Wilson estimate: 49.91 Å² / R_pim(I) all: 0.07 / R_rim(I) all: 0.179 / R_sym value: 0.15 / Net I/av σ(I): 4.4 / Net I/σ(I): 9.3 / Num. measured all: 343658

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	% possible all
2.822-2.97	6.8	0.702	1.1	7581	0.323	0.844	0.702	100
2.97-3.15	6.5	0.484	1.6	7148	0.229	0.585	0.484	100
3.15-3.37	6.6	0.33	2.3	6722	0.154	0.397	0.33	100
3.37-3.64	6.8	0.216	3.4	6294	0.099	0.259	0.216	100
3.64-3.99	6.6	0.148	4.7	5794	0.07	0.179	0.148	100
3.99-4.46	6.3	0.113	5.5	5272	0.054	0.135	0.113	99.9
4.46-5.15	6.7	0.096	6.7	4665	0.043	0.112	0.096	100
5.15-6.31	6.4	0.097	7.1	3997	0.045	0.113	0.097	100
6.31-8.92	6.4	0.068	8.4	3133	0.031	0.078	0.068	99.9
8.92-34.023	5.9	0.051	10.1	1784	0.024	0.059	0.051	97.8

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2D0T

2d0t

Resolution: 2.822→34.023 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.81

	R_factor	Num. reflection	% reflection
R_free	0.2718	2666	5.1 %
R_work	0.2107	-	-
obs	0.2138	52263	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 162.99 Å² / B_iso mean: 48.99 Å² / B_iso min: 3.17 Å²

Refinement step

Cycle: final / Resolution: 2.822→34.023 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10801	0	192	0	10993
B_iso mean	-	-	48.79	-	-
Num. residues	-	-	-	-	1472

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11280
X-RAY DIFFRACTION	f_angle_d	1.335	15437
X-RAY DIFFRACTION	f_chiral_restr	0.054	1728
X-RAY DIFFRACTION	f_plane_restr	0.007	1968
X-RAY DIFFRACTION	f_dihedral_angle_d	14.43	3777

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 19

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8217-2.8729	0.3627	168	0.3071	2550	2718	100
2.8729-2.9282	0.3388	143	0.2812	2571	2714	100
2.9282-2.9879	0.3971	145	0.2683	2573	2718	100
2.9879-3.0528	0.2896	130	0.2519	2605	2735	100
3.0528-3.1238	0.3305	147	0.2476	2547	2694	100
3.1238-3.2019	0.2825	145	0.2549	2593	2738	100
3.2019-3.2884	0.3257	151	0.2521	2561	2712	100
3.2884-3.385	0.2961	120	0.2277	2609	2729	100
3.385-3.4942	0.3032	145	0.2223	2590	2735	100
3.4942-3.6189	0.2813	124	0.2201	2598	2722	100
3.6189-3.7637	0.29	156	0.2085	2566	2722	100
3.7637-3.9347	0.2304	135	0.1921	2605	2740	100
3.9347-4.1418	0.2345	124	0.1868	2613	2737	100
4.1418-4.4008	0.227	130	0.1714	2629	2759	100
4.4008-4.7398	0.2357	144	0.171	2626	2770	100
4.7398-5.2152	0.2271	131	0.1809	2639	2770	100
5.2152-5.9664	0.2757	142	0.2111	2664	2806	100
5.9664-7.5037	0.2797	139	0.2156	2670	2809	100
7.5037-34.0258	0.2479	147	0.2005	2788	2935	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4937	0.3989	0.8937	1.0422	0.6533	1.5975	-0.0326	0.0403	-0.2196	0.1893	-0.0428	-0.0729	0.5746	0.0511	0.0767	0.5146	0.1119	-0.0459	0.3925	0.0274	0.417	53.5429	143.0115	-13.8153
2	0.3248	-0.2441	0.8394	1.4947	0.496	2.8771	0.0669	0.099	-0.0774	-0.1769	-0.1493	-0.1516	0.1456	0.427	0.196	0.3707	0.1057	0.0027	0.3748	-0.009	0.35	53.6391	149.9258	-12.8104
3	0.7648	0.1253	-0.0265	0.0421	0.1184	2.004	0.0212	-0.158	0.0255	0	-0.1043	-0.0301	-0.1626	0.0897	-0.0019	0.4433	0.0614	-0.0251	0.3603	-0.0369	0.3499	48.2386	159.3067	-1.0956
4	2.4704	0.0493	-0.4689	0.1598	-0.2422	3.1734	0.1317	-0.121	0.245	-0.3805	-0.1289	0.3382	-0.8852	-0.5383	-0.0696	0.6267	-0.0045	-0.033	0.4586	0.0028	0.3192	36.8279	164.9264	-4.4269
5	1.0563	-0.6595	0.1129	0.7385	0.3007	2.4877	0.0994	-0.1839	0.2196	-0.0561	-0.1538	0.0386	-0.7814	-0.3651	-0.0093	0.6593	0.0883	-0.0252	0.4393	-0.0311	0.3539	42.7724	167.9194	5.0664
6	2.0795	0.6811	-0.7278	1.1295	-1.5652	2.9619	-0.1895	0.4506	-0.2574	-0.424	0.2393	-0.4543	0.8073	-0.1567	-0.0176	0.7158	0.0136	0.026	0.3298	-0.0707	0.4141	13.411	142.623	-2.2953
7	1.2148	0.6642	0.0275	0.7519	-0.2769	2.451	-0.0499	-0.3487	-0.0407	0.188	-0.0709	0.152	0.2118	-0.0724	0.1165	0.3726	-0.036	-0.0269	0.3337	0.0072	0.3647	6.8781	144.3225	18.9549
8	0.4244	-0.0664	-0.8486	0.2591	-0.4923	2.6902	0.0027	0.084	0.0323	-0.1936	-0.0413	0.1059	-0.0261	-0.259	0.1087	0.4122	-0.0579	0.0084	0.3275	-0.0201	0.3345	8.7	153.222	-1.1257
9	0.0274	-0.1703	-0.2141	1.0762	-0.3399	2.5404	0.0645	0.0031	0.247	0.1098	-0.0621	0.1335	-0.4036	0.2126	-0.0512	0.5173	-0.0007	0.0057	0.4395	-0.0229	0.3827	19.6689	159.3314	8.5806
10	1.5142	0.4073	-0.2833	1.8589	-0.71	0.3155	0.0898	0.4004	-0.3465	-0.0193	-0.4408	-0.6128	-0.0832	0.4816	0.1902	0.5947	0.0265	0.0073	0.5543	0.0223	0.4535	27.5768	158.2513	-11.68
11	1.1475	-0.3849	-0.8612	0.959	0.0728	1.9619	0.2141	0.2182	-0.1709	-0.2693	-0.1147	-0.0359	-0.7654	-0.2226	-0.1599	0.3207	-0.0091	0.0497	0.3331	-0.0203	0.3415	11.7582	167.6899	-9.9773
12	1.807	0.5804	-0.6651	1.3581	-0.5799	2.5056	0.1908	-0.1279	0.3049	0.212	0.1184	0.1318	-0.3706	0.3166	-0.1385	0.6299	-0.0127	0.0548	0.355	0.0145	0.3822	12.2412	172.957	-0.2047
13	0.7795	0.827	0.3142	1.4145	0.1254	1.2524	0.1805	-0.0817	0.102	0.2258	-0.0913	0.1451	0.1117	0.0281	-0.0212	0.4254	0.133	0.0258	0.4371	-0.0182	0.4141	0.0843	191.9987	8.2321
14	1.7715	0.074	-0.4111	0.6433	-0.5471	1.4311	-0.0696	-0.0243	-0.1235	0.001	0.0779	0.1052	0.2873	0.147	-0.0109	0.3029	0.0701	0.0109	0.3125	-0.0291	0.4214	2.0658	193.4906	1.9268
15	1.4562	0.8169	-0.207	1.7259	0.4939	0.4454	-0.032	0.2781	0.035	-0.3422	0.0776	-0.094	0.1139	0.1681	0.0181	0.3468	0.0464	0.0594	0.4275	0.0155	0.361	8.3652	206.2527	-5.6171
16	1.8964	0.0481	-1.1592	0.3469	0.9262	3.3986	0.2141	-0.1839	0.8666	-0.2672	0.1139	0.2012	-0.7009	-0.1197	-0.2638	0.1946	0.0427	0.0326	0.254	0.0773	0.6558	8.8758	224.2366	-3.0446
17	0.9416	-0.3743	0.7437	2.6132	1.1201	1.416	0.0283	0.5297	0.1827	-0.6504	-0.0836	-0.2585	0.0013	-0.0577	-0.0335	0.7019	-0.1079	0.0092	0.6751	0.1133	0.4548	15.1166	210.1652	-16.578
18	0.7508	-0.5162	0.6715	0.7588	-0.681	2.0741	0.2147	0.0761	0.0689	0.1379	-0.1839	-0.2508	0.2657	0.0961	-0.0645	0.5203	-0.0705	-0.0626	0.4141	0.0107	0.4171	59.121	195.2712	-9.0003
19	1.8908	0.6572	0.2508	7.3313	0.8337	1.0733	0.194	-0.358	-0.3137	0.8535	-0.0259	-0.3452	0.3205	-0.077	0.0531	0.189	-0.0311	-0.118	0.2256	-0.0516	0.5218	68.0696	193.4447	-0.9287
20	1.1649	0.0809	-0.163	1.8904	-0.214	2.0393	0.1361	0.2194	0.1297	0.2539	0.0812	0.2999	0.5958	-0.3336	0.1336	0.2349	-0.122	0.0587	0.4562	0.0477	0.4092	43.304	206.7083	-2.6127
21	1.2016	-0.8501	-0.2787	1.0928	0.4121	0.8325	-0.0512	-0.1888	0.2282	0.7685	-0.0012	-0.3067	0.3944	-0.0485	-0.1255	0.6284	-0.0701	-0.003	0.4676	-0.0219	0.5029	56.2418	210.6018	5.7459
22	0.6644	-0.346	0.0631	3.1064	-1.5911	1.3597	0.3149	-0.359	0.0674	0.6313	-0.0861	0.4298	0.2335	0.0405	-0.0624	0.7375	-0.1197	0.0695	0.5725	-0.0769	0.4222	43.4249	212.1709	14.4971

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 72 )	A	12 - 72
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 159 )	A	73 - 159
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 160 through 277 )	A	160 - 277
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 278 through 300 )	A	278 - 300
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 301 through 401 )	A	301 - 401
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 12 through 33 )	B	12 - 33
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 34 through 104 )	B	34 - 104
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 105 through 240 )	B	105 - 240
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 241 through 300 )	B	241 - 300
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 301 through 325 )	B	301 - 325
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 326 through 353 )	B	326 - 353
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 354 through 401 )	B	354 - 401
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 12 through 72 )	C	12 - 72
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 73 through 159 )	C	73 - 159
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 160 through 300 )	C	160 - 300
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 301 through 325 )	C	301 - 325
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 326 through 401 )	C	326 - 401
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 12 through 92 )	D	12 - 92
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 93 through 117 )	D	93 - 117
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 118 through 220 )	D	118 - 220
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 221 through 325 )	D	221 - 325
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 326 through 401 )	D	326 - 401

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